# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Tue Jun  9 02:51:39 2020
#   Inital geometry file: a 120 line input string
#   Ligand name: methyl 4'-(alpha-D-mannopyranosyloxy)biphenyl-3-carboxylate
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COC(=O)c1cccc(c1)c2ccc(O[C@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]3O)cc2
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 ZH1  ZH1  'methyl 4'-(alpha-D-mannopyranosyloxy)biphenyl-3-carboxylate'  ligand  50  28  .  2021-08-25  2021-08-25  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_ZH1
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 ZH1  C1    C  CR16  0  -0.225   5.2224   2.4958  -0.1938
 ZH1  C2    C  CR16  0  -0.307   3.8381   2.4348  -0.2295
 ZH1  C3    C  CR16  0  -0.295   0.9147   2.1508   0.4020
 ZH1  C4    C  CR16  0  -0.301   1.0368   0.0798  -0.7756
 ZH1  C5    C  CR16  0  -0.284   5.9744   1.3387  -0.0654
 ZH1  C6    C  CR16  0  -0.336  -0.4652   2.0974   0.3576
 ZH1  C7    C  CR16  0  -0.344  -0.3482   0.0048  -0.8207
 ZH1  C8    C  CR16  0  -0.334   3.9357   0.0552   0.0010
 ZH1  C9    C  CR6   0   0.071   1.6977   1.1454  -0.1696
 ZH1  C10   C  CR6   0   0.120   3.1713   1.2116  -0.1311
 ZH1  C11   C  CR6   0  -0.061   5.3259   0.1090   0.0315
 ZH1  C12   C  CR6   0   0.379  -1.1090   1.0270  -0.2610
 ZH1  C13   C  C     0   0.598   6.0669  -1.1706   0.1812
 ZH1  C14   C  CH1   0   0.003  -5.3030   0.6665   0.1891
 ZH1  C15   C  CH1   0   0.028  -5.2601  -0.7686   0.7043
 ZH1  C16   C  CH1   0  -0.022  -4.6165   0.7705  -1.1706
 ZH1  C17   C  CH1   0  -0.014  -3.8152  -1.2702   0.7202
 ZH1  C18   C  CH1   0   0.202  -3.2036   0.1867  -1.0659
 ZH1  C19   C  CH3   0  -0.424   8.1932  -2.1627   0.3560
 ZH1  C20   C  CH2   0  -0.159  -3.7373  -2.7447   1.0547
 ZH1  O21   O  O     0  -0.447   5.5321  -2.2499   0.2716
 ZH1  O22   O  O2    0  -0.488  -3.2152  -1.1021  -0.5558
 ZH1  O23   O  OH1   0  -0.672  -6.6537   1.0588   0.1378
 ZH1  O24   O  OH1   0  -0.675  -5.7527  -0.8481   2.0202
 ZH1  O25   O  OH1   0  -0.665  -5.3652   0.0368  -2.1033
 ZH1  O26   O  OH1   0  -0.667  -2.3841  -3.1212   1.1449
 ZH1  O27   O  O2    0  -0.502  -2.4616   1.0772  -0.2653
 ZH1  O28   O  O2    0  -0.456   7.3777  -1.0006   0.2058
 ZH1  H1    H  HCR6  0   0.267   5.7192   3.4532  -0.2774
 ZH1  H2    H  HCR6  0   0.263   3.2714   3.3491  -0.3545
 ZH1  H3    H  HCR6  0   0.258   1.3851   2.9870   0.9035
 ZH1  H4    H  HCR6  0   0.260   1.6059  -0.7160  -1.2394
 ZH1  H5    H  HCR6  0   0.266   7.0529   1.4051  -0.0433
 ZH1  H6    H  HCR6  0   0.267  -1.0537   2.8883   0.8050
 ZH1  H7    H  HCR6  0   0.285  -0.8051  -0.8564  -1.2858
 ZH1  H8    H  HCR6  0   0.261   3.4435  -0.9037   0.1010
 ZH1  H14   H  HCH1  0   0.231  -4.7470   1.2946   0.8978
 ZH1  H15   H  HCH1  0   0.215  -5.8459  -1.4075   0.0268
 ZH1  H16   H  HCH1  0   0.240  -4.5362   1.8265  -1.4620
 ZH1  H17   H  HCH1  0   0.230  -3.2579  -0.7066   1.4821
 ZH1  H18   H  HCH1  0   0.264  -2.7494   0.1111  -2.0617
 ZH1  H19   H  HCH3  0   0.242   7.9830  -2.6771   1.2932
 ZH1  H19A  H  HCH3  0   0.242   8.0555  -2.8546  -0.4743
 ZH1  H19B  H  HCH3  0   0.255   9.2187  -1.8063   0.3623
 ZH1  H20   H  HCH2  0   0.212  -4.2670  -2.9123   1.9985
 ZH1  H20A  H  HCH2  0   0.196  -4.2692  -3.3155   0.2805
 ZH1  HO23  H  HOH1  0   0.458  -6.6994   2.0191   0.1694
 ZH1  HO24  H  HOH1  0   0.453  -6.6527  -0.5058   2.0177
 ZH1  HO25  H  HOH1  0   0.458  -5.0520   0.2509  -2.9875
 ZH1  HO26  H  HOH1  0   0.456  -2.3530  -4.0367   1.4359

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 ZH1  C2   C1    aromatic  1.386  0.020  1.386
 ZH1  C1   C5    aromatic  1.386  0.020  1.386
 ZH1  C1   H1    single    0.930  0.020  1.080
 ZH1  C2   C10   aromatic  1.397  0.020  1.397
 ZH1  C2   H2    single    0.930  0.020  1.080
 ZH1  C6   C3    aromatic  1.382  0.020  1.382
 ZH1  C3   C9    aromatic  1.397  0.020  1.397
 ZH1  C3   H3    single    0.930  0.020  1.080
 ZH1  C9   C4    aromatic  1.393  0.020  1.393
 ZH1  C7   C4    aromatic  1.388  0.020  1.388
 ZH1  C4   H4    single    0.930  0.020  1.080
 ZH1  C5   C11   aromatic  1.394  0.020  1.394
 ZH1  C5   H5    single    0.930  0.020  1.080
 ZH1  C6   C12   aromatic  1.394  0.020  1.394
 ZH1  C6   H6    single    0.930  0.020  1.080
 ZH1  C12  C7    aromatic  1.392  0.020  1.392
 ZH1  C7   H7    single    0.930  0.020  1.080
 ZH1  C10  C8    aromatic  1.393  0.020  1.393
 ZH1  C8   C11   aromatic  1.392  0.020  1.392
 ZH1  C8   H8    single    0.930  0.020  1.080
 ZH1  C9   C10   single    1.476  0.020  1.476
 ZH1  C11  C13   single    1.486  0.020  1.486
 ZH1  O27  C12   single    1.354  0.020  1.354
 ZH1  O28  C13   single    1.322  0.020  1.322
 ZH1  C13  O21   double    1.208  0.020  1.208
 ZH1  O23  C14   single    1.408  0.020  1.408
 ZH1  C14  C16   single    1.527  0.020  1.527
 ZH1  C14  C15   single    1.525  0.020  1.525
 ZH1  C14  H14   single    0.970  0.020  1.090
 ZH1  O24  C15   single    1.407  0.020  1.407
 ZH1  C15  C17   single    1.530  0.020  1.530
 ZH1  C15  H15   single    0.970  0.020  1.090
 ZH1  C16  C18   single    1.532  0.020  1.532
 ZH1  C16  O25   single    1.403  0.020  1.403
 ZH1  C16  H16   single    0.970  0.020  1.090
 ZH1  C17  O22   single    1.420  0.020  1.420
 ZH1  C17  C20   single    1.514  0.020  1.514
 ZH1  C17  H17   single    0.970  0.020  1.090
 ZH1  O27  C18   single    1.409  0.020  1.409
 ZH1  C18  O22   single    1.386  0.020  1.386
 ZH1  C18  H18   single    0.970  0.020  1.090
 ZH1  O28  C19   single    1.428  0.020  1.428
 ZH1  C19  H19   single    0.970  0.020  1.090
 ZH1  C19  H19A  single    0.970  0.020  1.090
 ZH1  C19  H19B  single    0.970  0.020  1.090
 ZH1  C20  O26   single    1.408  0.020  1.408
 ZH1  C20  H20   single    0.970  0.020  1.090
 ZH1  C20  H20A  single    0.970  0.020  1.090
 ZH1  O23  HO23  single    0.850  0.020  0.980
 ZH1  O24  HO24  single    0.850  0.020  0.980
 ZH1  O25  HO25  single    0.850  0.020  0.980
 ZH1  O26  HO26  single    0.850  0.020  0.980

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 ZH1  H1    C1   C5    119.79  3.000
 ZH1  H1    C1   C2    119.70  3.000
 ZH1  C5    C1   C2    120.50  3.000
 ZH1  H2    C2   C10   119.85  3.000
 ZH1  H2    C2   C1    119.24  3.000
 ZH1  C10   C2   C1    120.90  3.000
 ZH1  H3    C3   C9    120.13  3.000
 ZH1  H3    C3   C6    118.60  3.000
 ZH1  C9    C3   C6    121.26  3.000
 ZH1  H4    C4   C9    119.95  3.000
 ZH1  H4    C4   C7    118.10  3.000
 ZH1  C9    C4   C7    121.95  3.000
 ZH1  H5    C5   C11   121.14  3.000
 ZH1  H5    C5   C1    119.48  3.000
 ZH1  C11   C5   C1    119.38  3.000
 ZH1  H6    C6   C12   119.56  3.000
 ZH1  H6    C6   C3    120.09  3.000
 ZH1  C12   C6   C3    120.35  3.000
 ZH1  H7    C7   C12   121.84  3.000
 ZH1  H7    C7   C4    118.63  3.000
 ZH1  C12   C7   C4    119.52  3.000
 ZH1  H8    C8   C11   119.11  3.000
 ZH1  H8    C8   C10   119.66  3.000
 ZH1  C11   C8   C10   121.22  3.000
 ZH1  C10   C9   C4    121.31  3.000
 ZH1  C10   C9   C3    121.12  3.000
 ZH1  C4    C9   C3    117.57  3.000
 ZH1  C9    C10  C8    120.89  3.000
 ZH1  C9    C10  C2    120.95  3.000
 ZH1  C8    C10  C2    118.16  3.000
 ZH1  C13   C11  C8    117.84  3.000
 ZH1  C13   C11  C5    122.32  3.000
 ZH1  C8    C11  C5    119.84  3.000
 ZH1  O27   C12  C7    124.90  3.000
 ZH1  O27   C12  C6    115.76  3.000
 ZH1  C7    C12  C6    119.34  3.000
 ZH1  O28   C13  O21   123.54  3.000
 ZH1  O21   C13  C11   123.78  3.000
 ZH1  O28   C13  C11   112.68  3.000
 ZH1  H14   C14  O23   110.48  3.000
 ZH1  H14   C14  C16   107.95  3.000
 ZH1  O23   C14  C16   112.34  3.000
 ZH1  H14   C14  C15   107.81  3.000
 ZH1  C16   C14  C15   110.63  3.000
 ZH1  O23   C14  C15   107.55  3.000
 ZH1  H15   C15  O24   110.89  3.000
 ZH1  H15   C15  C17   108.60  3.000
 ZH1  O24   C15  C17   107.60  3.000
 ZH1  H15   C15  C14   108.87  3.000
 ZH1  C17   C15  C14   109.79  3.000
 ZH1  O24   C15  C14   111.05  3.000
 ZH1  H16   C16  O25   111.43  3.000
 ZH1  H16   C16  C18   108.48  3.000
 ZH1  O25   C16  C18   109.77  3.000
 ZH1  H16   C16  C14   109.55  3.000
 ZH1  O25   C16  C14   108.45  3.000
 ZH1  C18   C16  C14   109.13  3.000
 ZH1  H17   C17  O22   110.35  3.000
 ZH1  H17   C17  C20   108.67  3.000
 ZH1  O22   C17  C20   106.98  3.000
 ZH1  H17   C17  C15   108.54  3.000
 ZH1  C20   C17  C15   111.73  3.000
 ZH1  O22   C17  C15   110.54  3.000
 ZH1  H18   C18  O27   109.96  3.000
 ZH1  H18   C18  O22   105.87  3.000
 ZH1  O27   C18  O22   112.52  3.000
 ZH1  H18   C18  C16   110.24  3.000
 ZH1  O22   C18  C16   111.82  3.000
 ZH1  O27   C18  C16   106.48  3.000
 ZH1  H19B  C19  H19A  109.41  3.000
 ZH1  H19B  C19  H19   109.40  3.000
 ZH1  H19A  C19  H19   109.35  3.000
 ZH1  H19B  C19  O28   105.84  3.000
 ZH1  H19A  C19  O28   111.38  3.000
 ZH1  H19   C19  O28   111.38  3.000
 ZH1  H20A  C20  H20   107.07  3.000
 ZH1  H20A  C20  O26   111.81  3.000
 ZH1  H20   C20  O26   111.64  3.000
 ZH1  H20A  C20  C17   108.98  3.000
 ZH1  H20   C20  C17   108.33  3.000
 ZH1  O26   C20  C17   108.91  3.000
 ZH1  C18   O22  C17   116.38  3.000
 ZH1  HO23  O23  C14   108.82  3.000
 ZH1  HO24  O24  C15   107.74  3.000
 ZH1  HO25  O25  C16   108.71  3.000
 ZH1  HO26  O26  C20   107.77  3.000
 ZH1  C18   O27  C12   120.31  3.000
 ZH1  C19   O28  C13   117.63  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 ZH1  CONST_01  C8   C10  C2   C1     0.00   0.0  0
 ZH1  CONST_02  C9   C10  C2   C1   180.00   0.0  0
 ZH1  CONST_03  C8   C11  C5   C1     0.00   0.0  0
 ZH1  CONST_04  C11  C5   C1   C2     0.00   0.0  0
 ZH1  CONST_05  C11  C8   C10  C2     0.00   0.0  0
 ZH1  CONST_08  C7   C12  C6   C3     0.00   0.0  0
 ZH1  CONST_09  C7   C4   C9   C3     0.00   0.0  0
 ZH1  CONST_11  C6   C3   C9   C4     0.00   0.0  0
 ZH1  CONST_13  C6   C12  C7   C4     0.00   0.0  0
 ZH1  CONST_14  C10  C2   C1   C5     0.00   0.0  0
 ZH1  CONST_15  C10  C8   C11  C5     0.00   0.0  0
 ZH1  CONST_16  C10  C9   C3   C6   180.00   0.0  0
 ZH1  CONST_17  C10  C9   C4   C7   180.00   0.0  0
 ZH1  CONST_18  C12  C6   C3   C9     0.00   0.0  0
 ZH1  CONST_19  C12  C7   C4   C9     0.00   0.0  0
 ZH1  CONST_20  C11  C8   C10  C9   180.00   0.0  0
 ZH1  CONST_21  C13  C11  C5   C1   180.00   0.0  0
 ZH1  CONST_22  O27  C12  C6   C3   180.00   0.0  0
 ZH1  CONST_23  O27  C12  C7   C4   180.00   0.0  0
 ZH1  CONST_24  C13  C11  C8   C10  180.00   0.0  0
 ZH1  CONST_25  H5   C5   C1   C2   180.00   0.0  0
 ZH1  CONST_26  H8   C8   C10  C2   180.00   0.0  0
 ZH1  CONST_27  H4   C4   C9   C3   180.00   0.0  0
 ZH1  CONST_28  H3   C3   C9   C4   180.00   0.0  0
 ZH1  CONST_29  H2   C2   C1   C5   180.00   0.0  0
 ZH1  CONST_30  H7   C7   C12  C6   180.00   0.0  0
 ZH1  CONST_31  H6   C6   C12  C7   180.00   0.0  0
 ZH1  CONST_32  H1   C1   C2   C10  180.00   0.0  0
 ZH1  Var_01    O28  C13  C11  C5    -0.20  30.0  2
 ZH1  Var_02    H19  C19  O28  C13  -60.60  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 ZH1  chir_01  C14  O23  C16  C15  positiv
 ZH1  chir_02  C15  O24  C17  C14  positiv
 ZH1  chir_03  C16  O25  C14  C18  negativ
 ZH1  chir_04  C17  O22  C15  C20  negativ
 ZH1  chir_05  C18  O27  O22  C16  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 ZH1  plan-1  C1   0.020
 ZH1  plan-1  C2   0.020
 ZH1  plan-1  C5   0.020
 ZH1  plan-1  C8   0.020
 ZH1  plan-1  C9   0.020
 ZH1  plan-1  C10  0.020
 ZH1  plan-1  C11  0.020
 ZH1  plan-1  C13  0.020
 ZH1  plan-1  H1   0.020
 ZH1  plan-1  H2   0.020
 ZH1  plan-1  H5   0.020
 ZH1  plan-1  H8   0.020
 ZH1  plan-2  C3   0.020
 ZH1  plan-2  C4   0.020
 ZH1  plan-2  C6   0.020
 ZH1  plan-2  C7   0.020
 ZH1  plan-2  C9   0.020
 ZH1  plan-2  C10  0.020
 ZH1  plan-2  C12  0.020
 ZH1  plan-2  O27  0.020
 ZH1  plan-2  H3   0.020
 ZH1  plan-2  H4   0.020
 ZH1  plan-2  H6   0.020
 ZH1  plan-2  H7   0.020
 ZH1  plan-3  C11  0.020
 ZH1  plan-3  C13  0.020
 ZH1  plan-3  O21  0.020
 ZH1  plan-3  O28  0.020

